MolNFT v1 · #93568 · protein
Crystal structure of plp-soaked hmp synthase THI5 from S. cerevisiae
4H6D · Pyrimidine precursor biosynthesis enzyme THI5: “Crystal structure of plp-soaked hmp synthase THI5 from S. cerevisiae”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.81). MolNFT v1 #93568 on GenesisL1: 3D…
- PDB
- 4H6D
- Type
- protein
- Length
- 2,602 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrimidine precursor biosynthesis enzyme THI5
- UniProt
- P43534
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 330 | 48% helix, 17% strand | P43534 |
| A | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 314 | 47% helix, 17% strand | P43534 |
| B | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 329 | 47% helix, 17% strand | P43534 |
| C | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 335 | 48% helix, 16% strand | P43534 |
| D | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 333 | 47% helix, 17% strand | P43534 |
| E | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 302 | 46% helix, 18% strand | P43534 |
| G | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 331 | 47% helix, 17% strand | P43534 |
| H | Pyrimidine precursor biosynthesis enzyme THI5 | protein | 328 | 48% helix, 17% strand | P43534 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.81 | 0.86 | 62 | empty |
| 2 | 187 | 0.81 | 0.95 | 38 | empty |
| 3 | 204 | 0.80 | 0.94 | 39 | PLP |
| 4 | 203 | 0.80 | 0.94 | 33 | PLP |
| 5 | 234 | 0.79 | 0.92 | 36 | PLP |
Interfaces
13 interfaces between chains.
- B–H · 1430 Ų buried · 26 hydrogen bonds · protein-protein
- F–A · 1425 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 1420 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1417 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4H6D · Crystal structure of PLP-soaked HMP synthase Thi5 from S. cerevisiae · the same entry in another collection · chain H against H, TM-score 1.00
- P43534 · AlphaFold monomer V2.0 prediction for 4-amino-5-hydroxymethyl-2-methylpyrimidine… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P43534
- Elsewhere: RCSB PDB 4H6D · PDBe 4H6D · UniProt P43534
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